Open Microscopy Environment

Dear all,

I installed the OMERO server and I am able to connect via OMERO Windows client. Now I would like to continue with the installation of the web client, but have problems.

I installed the web client accordingly to https://www.openmicroscopy.org/site/sup ... uick-start but still have issues. When launching the web client via http://myservername:4080/ no login page appears. The browser is trying to connect several minutes. Not sure what the reason is.

Please find below some more details regarding the configuration:
- OS Red Hat Enterprise Linux Server release 6.3 (Santiago)
- Kernel 2.6.32-279.el6.x86_64
- Apache 2.2.15 is used as web server
- fastcgi is installed and activated

# httpd -M | grep cgi
cgi_module (shared)
fastcgi_module (shared)
Syntax OK

The configuration (output of ./omero config get):
omero.db.name=omero_database
omero.db.pass=***
omero.db.user=***
omero.web.application_server=fastcgi-tcp
omero.web.debug=True
omero.web.ping_interval=12000
omero.web.server_list=[["localhost", 4064, "omero"]]

What can I do now?

Thanks in advance for your assistance,
Andreas

Hi Andreas

With your current configuration you should be able to connect via whatever port Apache is listening on, e.g. http://myservername/ . Port 4080 is used internally by OMERO to communicate with Apache, and for the development server (not for production use). If that doesn't work could you provide your full Apache configuration:
/etc/httpd/conf/httpd.conf
/etc/httpd/conf.d/*.conf

Simon

Hi Simon,

Here is the requested configuration file content:

mod_fastcgi.conf:
LoadModule fastcgi_module modules/mod_fastcgi.so

php.conf:
#
# PHP is an HTML-embedded scripting language which attempts to make it
# easy for developers to write dynamically generated webpages.
#
<IfModule prefork.c>
LoadModule php5_module modules/libphp5.so
</IfModule>
<IfModule worker.c>
LoadModule php5_module modules/libphp5-zts.so
</IfModule>

#
# Cause the PHP interpreter to handle files with a .php extension.
#
AddHandler php5-script .php
AddType text/html .php

#
# Add index.php to the list of files that will be served as directory
# indexes.
#
DirectoryIndex index.php

#
# Uncomment the following line to allow PHP to pretty-print .phps
# files as PHP source code:
#
#AddType application/x-httpd-php-source .phps

welcome.conf:
#
# This configuration file enables the default "Welcome"
# page if there is no default index page present for
# the root URL. To disable the Welcome page, comment
# out all the lines below.
#
<LocationMatch "^/+$">
Options -Indexes
ErrorDocument 403 /error/noindex.html
</LocationMatch>


The content of the httpd.conf is large, therefore I pasted the OMERO section. In case you need more, let me know:
###
# apache config for omero
# this file should be loaded *after* ssl.conf
#
# -D options to control configurations
# OmeroWebClientRedirect - redirect / to /omero/webclient
# OmeroWebAdminRedirect - redirect / to /omero/webadmin
# OmeroForceSSL - redirect all http requests to https

###
### Example SSL stanza for OMERO.web created 2014-02-20 11:53:40.103155
###

# Eliminate overlap warnings with the default ssl vhost
# Requires SNI (http://wiki.apache.org/httpd/NameBasedSSLVHostsWithSNI) support
# most later versions of mod_ssl and OSes will support it
# if you see "You should not use name-based virtual hosts in conjunction with SSL!!"
# or similar start apache with -D DISABLE_SNI and modify ssl.conf
#<IfDefine !DISABLE_SNI>
# NameVirtualHost *:443
#</IfDefine>
#
## force https/ssl
#<IfDefine OmeroForceSSL>
# RewriteEngine on
# RewriteCond %{HTTPS} !on
# RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI} [L]
#</IfDefine>
#
#<VirtualHost _default_:443>
#
# ErrorLog logs/ssl_error_log
# TransferLog logs/ssl_access_log
# LogLevel warn
#
# SSLEngine on
# SSLProtocol all -SSLv2
# SSLCipherSuite ALL:!ADH:!EXPORT:!SSLv2:RC4+RSA:+HIGH:+MEDIUM:+LOW
# SSLCertificateFile /etc/pki/tls/certs/server.crt
# SSLCertificateKeyFile /etc/pki/tls/private/server.key
#
# # SSL Protocol Adjustments:
# SetEnvIf User-Agent ".*MSIE.*" # nokeepalive ssl-unclean-shutdown # downgrade-1.0 force-response-1.0
#
# # Per-Server Logging:
# CustomLog logs/ssl_request_log # "%t %h %{SSL_PROTOCOL}x %{SSL_CIPHER}x "%r" %b"
#
#</VirtualHost>

RewriteEngine on
RewriteRule ^/?$ /omero/ [R]

###
### Stanza for OMERO.web created 2014-02-20 11:53:40.103155
###
FastCGIExternalServer "/apps/test/omero/var/omero.fcgi" -host 0.0.0.0:4080

<Directory "/apps/test/omero/var">
Options -Indexes FollowSymLinks
Order allow,deny
Allow from all
</Directory>

<Directory "/apps/test/omero/lib/python/omeroweb/static">
Options -Indexes FollowSymLinks
Order allow,deny
Allow from all
</Directory>

Alias /static /apps/test/omero/lib/python/omeroweb/static
Alias /omero "/apps/test/omero/var/omero.fcgi/"


Thanks,
Andreas

Thanks Andreas. I've looked through your logs and it looks like OMERO.web has started, so it could be an apache problem. What do you see when you go to http://myservername/ ? I'd expect at least an Apache error page if nothing else.

Simon

Hi Simon,

Could this be the reason the the httpd is running under root (because it is a component of the RHEL system) and the OMERO server is running under another account? I made sure that there is not an access problem.

When I enter the URL http://mylocalserver/ I receive the login page. After having entered username / password and press the login button, I receive an error message "Internal Server Error".

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, root@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

Thanks,
Andreas

Hi Andreas

Having separate users for Apache and omero should be fine- it's a standard production setup. Could you upload your most recent OMERO web logs (OMEROweb.log and OMEROweb_request.log), and also your apache logs (/var/log/httpd/access_log, /var/log/httpd/error_log if it's a standard setup). Either as a zip attachment, or to https://www.openmicroscopy.org/qa2/qa/upload/ as before.

Thanks, Simon

Hi Simon,

log files are uploaded meanwhile.

Looking forward to your answer.

Thanks,
Andreas

error_log suggests Apache is unable to connect to OMERO. Could you check the permissions on the /apps/test/omero/var/ directory and all parent components, i.e. that it's accessible by the apache user (e.g. world-readable and world-executable)? Note omero.fcgi is a virtual file and doesn't actually exist, however the path to that location does need to be accessible.

Simon

Hi,

I made sure that the rights are set as you described and that the omero.fcgi file is deleted (was created with touch command). After restarting the httpd and the omero admin and omero web, the situation does not change.

Curious enough, when I try http://myomeroserver/ and I enter my username / password the error message appears. After trying this again http://myomeroserver/ teh picture of myself and the basic frame appears.

Thanks,
Andreas

Hi Andreas

Could you try clearing your browser cache and history? If that doesn't work could you upload your latest logs, as before?

Thanks, Simon